Metadata-Version: 2.1
Name: quantms-rescoring
Version: 0.0.1
Summary: quantms-rescoring: Python scripts and helpers for the quantMS workflow
License: MIT
Keywords: quantms,proteomics,mass-spectrometry,data-analysis,big data
Author: Yasset Perez-Riverol
Author-email: ypriverol@gmail.com
Requires-Python: >=3.8,<3.11
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Dist: click
Requires-Dist: deepLC (==2.2.38)
Requires-Dist: ms2rescore (==3.0.3)
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: protobuf (==3.19.6)
Requires-Dist: psm-utils (==0.8.3)
Requires-Dist: pygam
Requires-Dist: pyopenms
Requires-Dist: scipy (==1.13.1)
Project-URL: GitHub, https://github.com/bigbio/quantms-rescoring
Project-URL: LICENSE, https://github.com/bigbio/quantms-rescoring/blob/main/LICENSE
Project-URL: PyPi, https://pypi.org/project/quantms-rescoring/
Project-URL: Quantms, https://quantms.org
Description-Content-Type: text/markdown

# quantms-rescoring
    
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[![codecov](https://codecov.io/gh/bigbio/quantms-rescoring/branch/main/graph/badge.svg?token=3ZQZQ2ZQ2D)](https://codecov.io/gh/bigbio/quantms-rescoring)
[![PyPI version](https://badge.fury.io/py/quantms-rescoring.svg)](https://badge.fury.io/py/quantms-rescoring)
[![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)

quantms-rescoring is a Python tool for rescoring peptide-spectrum matches (PSMs) in idXML files. It is part of the quantms ecosystem package and leverages the MS²Rescore framework to improve identification confidence in proteomics data analysis.

## Features

- Enhanced Rescoring: Utilizes advanced rescoring engines like Percolator to refine PSM scores.
- Flexible Feature Generators: Supports feature extraction using tools like MS²PIP, DeepLC, and custom generators.
- Metadata Retention: Preserves essential metadata from the input idXML files.
- Error Handling: Skips invalid PSMs and logs issues for transparent processing.
- Seamless Integration: Built to integrate into proteomics workflows.

## Installation

To use quantms-rescoring, ensure the following dependencies are installed:

- Python 3.8+
- click
- pyopenms
- ms2rescore
- psm_utils

### Issues and Contributions

For any issues or contributions, please open an issue in the [GitHub repository](https://github.com/bigbio/quantms/issues) - we use the quantms repo to control all issues—or PR in the [GitHub repository](https://github.com/bigbio/quantms-rescoring/pulls). 


